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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-03-27, 11:28 CET based on data in: /home/benlloch/parkinson/analysis/fastqs_processed/fastqc_reports_after_proc

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        General Statistics

        Showing 168/168 rows and 3/6 columns.
        Sample NameDupsGCAvg lenMedian lenFailedSeqs
        SRR22002247_1_trim_polyA_trimmed_Q
        61.6%
        51.0%
        119bp
        121bp
        18%
        54.3M
        SRR22002247_2_trim_polyA_trimmed_Q
        58.3%
        51.0%
        119bp
        121bp
        18%
        54.3M
        SRR22002248_1_trim_polyA_trimmed_Q
        63.2%
        51.0%
        119bp
        121bp
        27%
        50.3M
        SRR22002248_2_trim_polyA_trimmed_Q
        59.9%
        51.0%
        119bp
        121bp
        18%
        50.3M
        SRR22002249_1_trim_polyA_trimmed_Q
        62.2%
        50.0%
        119bp
        121bp
        27%
        50.8M
        SRR22002249_2_trim_polyA_trimmed_Q
        59.3%
        50.0%
        119bp
        121bp
        18%
        50.8M
        SRR22002250_1_trim_polyA_trimmed_Q
        54.9%
        50.0%
        119bp
        121bp
        27%
        52.8M
        SRR22002250_2_trim_polyA_trimmed_Q
        52.2%
        50.0%
        119bp
        121bp
        18%
        52.8M
        SRR22002251_1_trim_polyA_trimmed_Q
        64.9%
        53.0%
        119bp
        121bp
        27%
        52.2M
        SRR22002251_2_trim_polyA_trimmed_Q
        62.0%
        53.0%
        119bp
        121bp
        18%
        52.2M
        SRR22002252_1_trim_polyA_trimmed_Q
        52.1%
        49.0%
        119bp
        121bp
        18%
        50.0M
        SRR22002252_2_trim_polyA_trimmed_Q
        48.4%
        49.0%
        119bp
        121bp
        0%
        50.0M
        SRR22002253_1_trim_polyA_trimmed_Q
        69.1%
        52.0%
        119bp
        121bp
        36%
        51.0M
        SRR22002253_2_trim_polyA_trimmed_Q
        66.4%
        52.0%
        119bp
        121bp
        18%
        51.0M
        SRR22002254_1_trim_polyA_trimmed_Q
        61.7%
        50.0%
        119bp
        121bp
        18%
        48.6M
        SRR22002254_2_trim_polyA_trimmed_Q
        58.7%
        50.0%
        119bp
        121bp
        18%
        48.6M
        SRR22002255_1_trim_polyA_trimmed_Q
        53.1%
        49.0%
        118bp
        121bp
        27%
        50.6M
        SRR22002255_2_trim_polyA_trimmed_Q
        50.3%
        49.0%
        118bp
        121bp
        18%
        50.6M
        SRR22002256_1_trim_polyA_trimmed_Q
        63.7%
        50.0%
        119bp
        121bp
        27%
        53.1M
        SRR22002256_2_trim_polyA_trimmed_Q
        60.8%
        51.0%
        119bp
        121bp
        18%
        53.1M
        SRR22002257_1_trim_polyA_trimmed_Q
        64.4%
        50.0%
        119bp
        121bp
        36%
        50.5M
        SRR22002257_2_trim_polyA_trimmed_Q
        61.8%
        51.0%
        119bp
        121bp
        18%
        50.5M
        SRR22002258_1_trim_polyA_trimmed_Q
        54.8%
        49.0%
        118bp
        121bp
        27%
        50.3M
        SRR22002258_2_trim_polyA_trimmed_Q
        52.0%
        49.0%
        119bp
        121bp
        18%
        50.3M
        SRR22002259_1_trim_polyA_trimmed_Q
        58.8%
        49.0%
        119bp
        121bp
        27%
        50.7M
        SRR22002259_2_trim_polyA_trimmed_Q
        55.7%
        50.0%
        119bp
        121bp
        18%
        50.7M
        SRR22002260_1_trim_polyA_trimmed_Q
        62.6%
        50.0%
        119bp
        121bp
        27%
        51.8M
        SRR22002260_2_trim_polyA_trimmed_Q
        60.0%
        51.0%
        119bp
        121bp
        18%
        51.8M
        SRR22002261_1_trim_polyA_trimmed_Q
        48.4%
        48.0%
        118bp
        121bp
        9%
        50.6M
        SRR22002261_2_trim_polyA_trimmed_Q
        45.4%
        48.0%
        119bp
        121bp
        0%
        50.6M
        SRR22002262_1_trim_polyA_trimmed_Q
        63.9%
        50.0%
        119bp
        121bp
        27%
        51.1M
        SRR22002262_2_trim_polyA_trimmed_Q
        61.1%
        51.0%
        119bp
        121bp
        18%
        51.1M
        SRR22002263_1_trim_polyA_trimmed_Q
        61.6%
        50.0%
        119bp
        121bp
        27%
        50.6M
        SRR22002263_2_trim_polyA_trimmed_Q
        57.7%
        50.0%
        119bp
        121bp
        18%
        50.6M
        SRR22002264_1_trim_polyA_trimmed_Q
        64.6%
        51.0%
        119bp
        121bp
        27%
        50.8M
        SRR22002264_2_trim_polyA_trimmed_Q
        61.6%
        52.0%
        119bp
        121bp
        18%
        50.8M
        SRR22002265_1_trim_polyA_trimmed_Q
        49.6%
        49.0%
        118bp
        121bp
        9%
        52.2M
        SRR22002265_2_trim_polyA_trimmed_Q
        46.2%
        49.0%
        118bp
        121bp
        0%
        52.2M
        SRR22002266_1_trim_polyA_trimmed_Q
        65.0%
        50.0%
        119bp
        121bp
        18%
        55.5M
        SRR22002266_2_trim_polyA_trimmed_Q
        62.6%
        50.0%
        119bp
        121bp
        18%
        55.5M
        SRR22002267_1_trim_polyA_trimmed_Q
        63.3%
        50.0%
        119bp
        121bp
        18%
        56.3M
        SRR22002267_2_trim_polyA_trimmed_Q
        60.6%
        50.0%
        119bp
        121bp
        18%
        56.3M
        SRR22002268_1_trim_polyA_trimmed_Q
        65.3%
        50.0%
        119bp
        121bp
        18%
        60.4M
        SRR22002268_2_trim_polyA_trimmed_Q
        62.6%
        50.0%
        119bp
        121bp
        18%
        60.4M
        SRR22002269_1_trim_polyA_trimmed_Q
        52.6%
        49.0%
        118bp
        121bp
        18%
        53.9M
        SRR22002269_2_trim_polyA_trimmed_Q
        49.7%
        49.0%
        118bp
        121bp
        9%
        53.9M
        SRR22002270_1_trim_polyA_trimmed_Q
        54.6%
        50.0%
        118bp
        121bp
        18%
        48.5M
        SRR22002270_2_trim_polyA_trimmed_Q
        51.1%
        50.0%
        119bp
        121bp
        18%
        48.5M
        SRR22002271_1_trim_polyA_trimmed_Q
        61.1%
        51.0%
        119bp
        121bp
        27%
        50.6M
        SRR22002271_2_trim_polyA_trimmed_Q
        58.4%
        51.0%
        119bp
        121bp
        18%
        50.6M
        SRR22002272_1_trim_polyA_trimmed_Q
        57.7%
        49.0%
        118bp
        121bp
        27%
        63.3M
        SRR22002272_2_trim_polyA_trimmed_Q
        55.0%
        49.0%
        119bp
        121bp
        18%
        63.3M
        SRR22002273_1_trim_polyA_trimmed_Q
        63.6%
        50.0%
        119bp
        121bp
        27%
        63.2M
        SRR22002273_2_trim_polyA_trimmed_Q
        61.0%
        50.0%
        119bp
        121bp
        18%
        63.2M
        SRR22002274_1_trim_polyA_trimmed_Q
        71.1%
        50.0%
        119bp
        121bp
        27%
        69.5M
        SRR22002274_2_trim_polyA_trimmed_Q
        68.5%
        50.0%
        119bp
        121bp
        18%
        69.5M
        SRR22002275_1_trim_polyA_trimmed_Q
        62.3%
        50.0%
        119bp
        121bp
        27%
        61.7M
        SRR22002275_2_trim_polyA_trimmed_Q
        59.7%
        50.0%
        119bp
        121bp
        18%
        61.7M
        SRR22002276_1_trim_polyA_trimmed_Q
        63.2%
        50.0%
        119bp
        121bp
        27%
        66.5M
        SRR22002276_2_trim_polyA_trimmed_Q
        60.8%
        50.0%
        119bp
        121bp
        18%
        66.5M
        SRR22002277_1_trim_polyA_trimmed_Q
        62.0%
        49.0%
        119bp
        121bp
        27%
        65.0M
        SRR22002277_2_trim_polyA_trimmed_Q
        59.7%
        50.0%
        119bp
        121bp
        18%
        65.0M
        SRR22002278_1_trim_polyA_trimmed_Q
        63.6%
        49.0%
        119bp
        121bp
        36%
        59.7M
        SRR22002278_2_trim_polyA_trimmed_Q
        61.0%
        50.0%
        119bp
        121bp
        18%
        59.7M
        SRR22002279_1_trim_polyA_trimmed_Q
        53.0%
        48.0%
        118bp
        121bp
        18%
        65.3M
        SRR22002279_2_trim_polyA_trimmed_Q
        50.2%
        48.0%
        119bp
        121bp
        9%
        65.3M
        SRR22002280_1_trim_polyA_trimmed_Q
        68.8%
        50.0%
        119bp
        121bp
        27%
        62.1M
        SRR22002280_2_trim_polyA_trimmed_Q
        65.1%
        51.0%
        119bp
        121bp
        18%
        62.1M
        SRR22002281_1_trim_polyA_trimmed_Q
        63.4%
        50.0%
        119bp
        121bp
        18%
        52.5M
        SRR22002281_2_trim_polyA_trimmed_Q
        60.4%
        51.0%
        119bp
        121bp
        18%
        52.5M
        SRR22002282_1_trim_polyA_trimmed_Q
        57.2%
        48.0%
        119bp
        121bp
        9%
        57.6M
        SRR22002282_2_trim_polyA_trimmed_Q
        53.3%
        48.0%
        119bp
        121bp
        9%
        57.6M
        SRR22002283_1_trim_polyA_trimmed_Q
        57.0%
        49.0%
        118bp
        121bp
        18%
        64.3M
        SRR22002283_2_trim_polyA_trimmed_Q
        53.3%
        49.0%
        119bp
        121bp
        18%
        64.3M
        SRR22002284_1_trim_polyA_trimmed_Q
        68.0%
        50.0%
        119bp
        121bp
        27%
        64.7M
        SRR22002284_2_trim_polyA_trimmed_Q
        63.9%
        50.0%
        119bp
        121bp
        18%
        64.7M
        SRR22002285_1_trim_polyA_trimmed_Q
        66.7%
        50.0%
        119bp
        121bp
        18%
        58.8M
        SRR22002285_2_trim_polyA_trimmed_Q
        62.6%
        50.0%
        119bp
        121bp
        18%
        58.8M
        SRR22002286_1_trim_polyA_trimmed_Q
        67.9%
        51.0%
        119bp
        121bp
        27%
        58.6M
        SRR22002286_2_trim_polyA_trimmed_Q
        64.5%
        51.0%
        119bp
        121bp
        18%
        58.6M
        SRR22002287_1_trim_polyA_trimmed_Q
        64.8%
        50.0%
        119bp
        121bp
        27%
        59.7M
        SRR22002287_2_trim_polyA_trimmed_Q
        61.4%
        50.0%
        119bp
        121bp
        18%
        59.7M
        SRR22002288_1_trim_polyA_trimmed_Q
        66.6%
        50.0%
        118bp
        121bp
        27%
        62.6M
        SRR22002288_2_trim_polyA_trimmed_Q
        62.7%
        50.0%
        119bp
        121bp
        18%
        62.6M
        SRR22002289_1_trim_polyA_trimmed_Q
        54.6%
        48.0%
        118bp
        121bp
        18%
        53.2M
        SRR22002289_2_trim_polyA_trimmed_Q
        50.4%
        48.0%
        118bp
        121bp
        9%
        53.2M
        SRR22002290_1_trim_polyA_trimmed_Q
        65.8%
        49.0%
        119bp
        121bp
        27%
        66.7M
        SRR22002290_2_trim_polyA_trimmed_Q
        61.6%
        49.0%
        119bp
        121bp
        18%
        66.7M
        SRR22002291_1_trim_polyA_trimmed_Q
        62.5%
        49.0%
        119bp
        121bp
        18%
        62.7M
        SRR22002291_2_trim_polyA_trimmed_Q
        57.9%
        49.0%
        119bp
        121bp
        18%
        62.7M
        SRR22002292_1_trim_polyA_trimmed_Q
        61.3%
        50.0%
        119bp
        121bp
        27%
        55.3M
        SRR22002292_2_trim_polyA_trimmed_Q
        57.4%
        50.0%
        119bp
        121bp
        18%
        55.3M
        SRR22002293_1_trim_polyA_trimmed_Q
        60.6%
        48.0%
        118bp
        121bp
        18%
        67.2M
        SRR22002293_2_trim_polyA_trimmed_Q
        56.3%
        48.0%
        119bp
        121bp
        18%
        67.2M
        SRR22002294_1_trim_polyA_trimmed_Q
        64.0%
        49.0%
        119bp
        121bp
        18%
        60.7M
        SRR22002294_2_trim_polyA_trimmed_Q
        60.6%
        50.0%
        119bp
        121bp
        18%
        60.7M
        SRR22002295_1_trim_polyA_trimmed_Q
        63.6%
        51.0%
        119bp
        121bp
        9%
        64.2M
        SRR22002295_2_trim_polyA_trimmed_Q
        59.5%
        51.0%
        119bp
        121bp
        18%
        64.2M
        SRR22002296_1_trim_polyA_trimmed_Q
        49.6%
        47.0%
        118bp
        121bp
        0%
        74.9M
        SRR22002296_2_trim_polyA_trimmed_Q
        46.1%
        47.0%
        119bp
        121bp
        0%
        74.9M
        SRR22002297_1_trim_polyA_trimmed_Q
        58.9%
        49.0%
        119bp
        121bp
        18%
        70.7M
        SRR22002297_2_trim_polyA_trimmed_Q
        55.5%
        49.0%
        119bp
        121bp
        18%
        70.7M
        SRR22002298_1_trim_polyA_trimmed_Q
        64.7%
        49.0%
        119bp
        121bp
        27%
        59.5M
        SRR22002298_2_trim_polyA_trimmed_Q
        61.1%
        50.0%
        119bp
        121bp
        18%
        59.5M
        SRR22002299_1_trim_polyA_trimmed_Q
        64.7%
        49.0%
        119bp
        121bp
        18%
        59.0M
        SRR22002299_2_trim_polyA_trimmed_Q
        60.6%
        49.0%
        119bp
        121bp
        18%
        59.0M
        SRR22002300_1_trim_polyA_trimmed_Q
        49.1%
        48.0%
        118bp
        121bp
        9%
        51.2M
        SRR22002300_2_trim_polyA_trimmed_Q
        45.4%
        48.0%
        119bp
        121bp
        9%
        51.2M
        SRR22002301_1_trim_polyA_trimmed_Q
        42.3%
        48.0%
        118bp
        121bp
        0%
        57.9M
        SRR22002301_2_trim_polyA_trimmed_Q
        38.3%
        48.0%
        119bp
        121bp
        9%
        57.9M
        SRR22002302_1_trim_polyA_trimmed_Q
        52.5%
        48.0%
        119bp
        121bp
        9%
        58.2M
        SRR22002302_2_trim_polyA_trimmed_Q
        48.1%
        49.0%
        119bp
        121bp
        0%
        58.2M
        SRR22002303_1_trim_polyA_trimmed_Q
        67.8%
        49.0%
        119bp
        121bp
        18%
        66.4M
        SRR22002303_2_trim_polyA_trimmed_Q
        64.4%
        49.0%
        119bp
        121bp
        18%
        66.4M
        SRR22002304_1_trim_polyA_trimmed_Q
        51.7%
        49.0%
        118bp
        121bp
        18%
        61.9M
        SRR22002304_2_trim_polyA_trimmed_Q
        48.4%
        49.0%
        119bp
        121bp
        0%
        61.9M
        SRR22002305_1_trim_polyA_trimmed_Q
        58.2%
        49.0%
        118bp
        121bp
        18%
        66.1M
        SRR22002305_2_trim_polyA_trimmed_Q
        54.5%
        50.0%
        119bp
        121bp
        18%
        66.1M
        SRR22002306_1_trim_polyA_trimmed_Q
        54.2%
        49.0%
        119bp
        121bp
        18%
        50.7M
        SRR22002306_2_trim_polyA_trimmed_Q
        50.2%
        49.0%
        119bp
        121bp
        18%
        50.7M
        SRR22002307_1_trim_polyA_trimmed_Q
        52.9%
        49.0%
        118bp
        121bp
        27%
        52.5M
        SRR22002307_2_trim_polyA_trimmed_Q
        49.6%
        49.0%
        118bp
        121bp
        9%
        52.5M
        SRR22002308_1_trim_polyA_trimmed_Q
        50.6%
        48.0%
        118bp
        121bp
        18%
        58.9M
        SRR22002308_2_trim_polyA_trimmed_Q
        46.6%
        48.0%
        119bp
        121bp
        0%
        58.9M
        SRR22002309_1_trim_polyA_trimmed_Q
        58.8%
        49.0%
        118bp
        121bp
        18%
        55.2M
        SRR22002309_2_trim_polyA_trimmed_Q
        54.6%
        49.0%
        119bp
        121bp
        18%
        55.2M
        SRR22002310_1_trim_polyA_trimmed_Q
        65.0%
        50.0%
        119bp
        121bp
        18%
        71.9M
        SRR22002310_2_trim_polyA_trimmed_Q
        60.6%
        50.0%
        119bp
        121bp
        18%
        71.9M
        SRR22002311_1_trim_polyA_trimmed_Q
        61.6%
        50.0%
        119bp
        121bp
        27%
        52.6M
        SRR22002311_2_trim_polyA_trimmed_Q
        57.5%
        50.0%
        119bp
        121bp
        18%
        52.6M
        SRR22002312_1_trim_polyA_trimmed_Q
        53.4%
        49.0%
        119bp
        121bp
        18%
        61.0M
        SRR22002312_2_trim_polyA_trimmed_Q
        49.3%
        49.0%
        119bp
        121bp
        9%
        61.0M
        SRR22002313_1_trim_polyA_trimmed_Q
        64.0%
        50.0%
        118bp
        121bp
        27%
        65.7M
        SRR22002313_2_trim_polyA_trimmed_Q
        59.9%
        50.0%
        119bp
        121bp
        18%
        65.7M
        SRR22002314_1_trim_polyA_trimmed_Q
        62.3%
        49.0%
        119bp
        121bp
        27%
        62.6M
        SRR22002314_2_trim_polyA_trimmed_Q
        58.3%
        50.0%
        119bp
        121bp
        18%
        62.6M
        SRR22002315_1_trim_polyA_trimmed_Q
        56.6%
        50.0%
        119bp
        121bp
        27%
        52.1M
        SRR22002315_2_trim_polyA_trimmed_Q
        53.2%
        50.0%
        119bp
        121bp
        18%
        52.1M
        SRR22002316_1_trim_polyA_trimmed_Q
        57.9%
        50.0%
        118bp
        121bp
        27%
        52.5M
        SRR22002316_2_trim_polyA_trimmed_Q
        54.2%
        50.0%
        118bp
        121bp
        18%
        52.5M
        SRR22002317_1_trim_polyA_trimmed_Q
        55.2%
        48.0%
        119bp
        121bp
        10%
        56.5M
        SRR22002317_2_trim_polyA_trimmed_Q
        49.3%
        48.0%
        119bp
        121bp
        0%
        56.5M
        SRR22002318_1_trim_polyA_trimmed_Q
        57.2%
        48.0%
        119bp
        121bp
        10%
        71.1M
        SRR22002318_2_trim_polyA_trimmed_Q
        51.8%
        48.0%
        118bp
        121bp
        10%
        71.1M
        SRR22002319_1_trim_polyA_trimmed_Q
        63.0%
        48.0%
        119bp
        121bp
        18%
        66.0M
        SRR22002319_2_trim_polyA_trimmed_Q
        57.6%
        49.0%
        119bp
        121bp
        9%
        66.0M
        SRR22002320_1_trim_polyA_trimmed_Q
        64.0%
        48.0%
        119bp
        121bp
        9%
        72.2M
        SRR22002320_2_trim_polyA_trimmed_Q
        59.7%
        49.0%
        119bp
        121bp
        9%
        72.2M
        SRR22002321_1_trim_polyA_trimmed_Q
        62.8%
        48.0%
        119bp
        121bp
        18%
        69.4M
        SRR22002321_2_trim_polyA_trimmed_Q
        57.4%
        49.0%
        119bp
        121bp
        9%
        69.4M
        SRR22002322_1_trim_polyA_trimmed_Q
        54.9%
        47.0%
        119bp
        121bp
        10%
        65.3M
        SRR22002322_2_trim_polyA_trimmed_Q
        49.8%
        47.0%
        119bp
        121bp
        0%
        65.3M
        SRR22002323_1_trim_polyA_trimmed_Q
        63.9%
        48.0%
        119bp
        121bp
        18%
        89.6M
        SRR22002323_2_trim_polyA_trimmed_Q
        57.9%
        48.0%
        119bp
        121bp
        9%
        89.6M
        SRR22002324_1_trim_polyA_trimmed_Q
        64.6%
        48.0%
        119bp
        121bp
        18%
        82.4M
        SRR22002324_2_trim_polyA_trimmed_Q
        58.9%
        49.0%
        119bp
        121bp
        9%
        82.4M
        SRR22002325_1_trim_polyA_trimmed_Q
        68.9%
        49.0%
        119bp
        121bp
        18%
        76.3M
        SRR22002325_2_trim_polyA_trimmed_Q
        63.6%
        49.0%
        119bp
        121bp
        9%
        76.3M
        SRR22002326_1_trim_polyA_trimmed_Q
        60.9%
        48.0%
        119bp
        121bp
        18%
        69.1M
        SRR22002326_2_trim_polyA_trimmed_Q
        54.9%
        49.0%
        119bp
        121bp
        9%
        69.1M
        SRR22002327_1_trim_polyA_trimmed_Q
        60.6%
        48.0%
        119bp
        121bp
        18%
        68.3M
        SRR22002327_2_trim_polyA_trimmed_Q
        55.2%
        49.0%
        119bp
        121bp
        9%
        68.3M
        SRR22002328_1_trim_polyA_trimmed_Q
        66.6%
        48.0%
        119bp
        121bp
        18%
        70.2M
        SRR22002328_2_trim_polyA_trimmed_Q
        60.5%
        49.0%
        119bp
        121bp
        9%
        70.2M
        SRR22002329_1_trim_polyA_trimmed_Q
        65.6%
        49.0%
        119bp
        121bp
        18%
        69.7M
        SRR22002329_2_trim_polyA_trimmed_Q
        59.7%
        49.0%
        119bp
        121bp
        9%
        69.7M
        SRR22002330_1_trim_polyA_trimmed_Q
        68.4%
        49.0%
        119bp
        121bp
        18%
        76.6M
        SRR22002330_2_trim_polyA_trimmed_Q
        63.1%
        49.0%
        119bp
        121bp
        9%
        76.6M

        FastQC

        Version: 0.12.1

        Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        GTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGA
        96
        38162244
        0.3781%
        CAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTT
        96
        28305125
        0.2804%
        AGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTT
        84
        17118482
        0.1696%
        CGTTCTCCTACAAATGGACCTTGAGAGCTTGTTTGGAGGTTCTAGCAGGG
        84
        17247254
        0.1709%
        GGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTC
        83
        19216240
        0.1904%
        GGATCGCTTGAGTCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGG
        82
        10778289
        0.1068%
        GGATCGCTTGAGCCCAGGAGTTCTGGGCTGTAGTGCGCTATGCCGATCGG
        82
        10561162
        0.1046%
        GCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCC
        78
        10860146
        0.1076%
        CTCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTG
        77
        8209730
        0.0813%
        ACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGT
        76
        13629742
        0.1350%
        GTGCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCATCAATATGGTG
        76
        8867045
        0.0879%
        CTCGGGAGGCTGAGGCTGGAGGATCGCTTGAGTCCAGGAGTTCTGGGCTG
        74
        7547358
        0.0748%
        CTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCCGACCTGGGCCGGTT
        68
        5997490
        0.0594%
        TACGTTCTCCTACAAATGGACCTTGAGAGCTTGTTTGGAGGTTCTAGCAG
        66
        6881450
        0.0682%
        TCGGGAGGCTGAGGTGGGAGGATCGCTTGAGCCCAGGAGTTCTGGGCTGT
        64
        5561324
        0.0551%
        AGTGGCTATTCACAGGCGCGATCCCACTACTGATCAGCACGGGAGTTTTG
        61
        6470780
        0.0641%
        GCGCTATGCCGATCGGGTGTCCGCACTAAGTTCGGCATCAATATGGTGAC
        60
        5756636
        0.0570%
        GCGATCCCACTACTGATCAGCACGGGAGTTTTGACCTGCTCCGTTTCCGA
        57
        6557721
        0.0650%
        CCTCCTTAGGCAACCTGGTGGTCCCCCGCTCCCGGGAGGTCACCATATTG
        54
        4393623
        0.0435%
        GCTCCCGGGAGGTCACCATATTGATGCCGAACTTAGTGCGGACACCCGAT
        54
        5360576
        0.0531%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        No samples found with any adapter contamination > 0.1%

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1